Scope Lipoprotein particle measures performed by nuclear magnetic resonance (NMR), and associated ratios, may be better markers for atherosclerosis risk than conventional lipid measures. The effect of two functional olive oils, one enriched with its polyphenols (FVOO, 500 ppm), and the other (FVOOT) with them (250 ppm) and those of thyme (250 ppm), versus a standard virgin olive oil (VOO), on lipoprotein particle atherogenic ratios and subclasses profiles was assessed. Methods and results In a randomized, double‐blind, crossover, controlled trial, 33 hypercholesterolemic individuals received 25 mL/day of VOO, FVOO, and FVOOT. Intervention periods were of 3 weeks separated by 2‐week washout periods. Lipoprotein particle counts and subclasses were measured by NMR. Polyphenols from olive oil and thyme modified the lipoprotein subclasses profile and decreased the total LDL particle/total HDL particle (HDL‐P), small HDL/large HDL, and HDL‐cholesterol/HDL‐P ratios, and decreased the lipoprotein insulin resistance index (LP‐IR) (p < 0.05). Conclusion Olive oil polyphenols, and those from thyme provided benefits on lipoprotein particle atherogenic ratios and subclasses profile distribution. Polyphenol‐enriched olive oil is a way of increasing the olive oil healthy properties while consuming the same amount of fat, as well as a useful and complementary tool for the management of cardiovascular risk individuals. Volunteers (n = 33) followed a 2‐week wash out period (WO; olive oil with a very low phenolic content) between the 3‐week interventions: VOO: Control Virgin Olive Oil (VOO). FVOO: Functional VOO enriched with phenolic compounds from VOO. FVOOT: FVOO enriched with polyphenols from VOO and thyme. Samples were analyzed by NMR. Main outcomes include an improvement in the lipoprotein subclasses profile and a decrease in LDL‐P/HLD‐P, HDL‐C/HDL‐P, and s‐HDL/l‐HDL atherogenic ratios, and in the LipoProtein‐Insulin Resistance Index.